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7. TRENDS TOWARDS THE PRODUCTION OF BIOLOGICALLY SAFE MARKER FREE TRANSGENIC PLANTS.

Author

QAMAR, Z., RIZWAN, M., RANI, R., SHAHZAD, R., JAMIL, S., FAHEEM, M., ABRO, S., and SHIMELIS, H.

Subjects
TRANSGENIC plants, PLANT genetic transformation, TETRAHYDROFOLATE dehydrogenase, CROPS, GENETIC transformation
Abstract

In the majority of plant biotechnology laboratories throughout the world, plant transformation is a common practice to improve several traits of plants, particularly grain yield. During the experiments, only a small percentage of cells transform in the targeted population. For selection of transformed cells, it is necessary to use the selectable markers such as Neomycin phosphotransferase (nptII), Chloramphenicolacetyle transferase (Cat), Hygromycin phosphotransferase (hph), Streptomycin phosphotransferase (spt), Phosphinothrycin acetyletransferase (pat) and Dihydrofolate reductase (dhf). The majority of these and other markers detoxify different antibiotics including paromomycin, kanamycin, hygromycin, neomycin, and streptomycin etc. But as these antibiotics become resistant, most of the markers raise serious safety concerns to human health. Additionally, in case of multiple genes transfer, it also limits the availability of these selectable markers. Keeping in view the limitations of selectable markers, production of marker-free transgenic plants is becoming the global trend. Current review explored the probabilities and prospects to cope with these issues. This review describes in detail the various plant transformation systems for the development of selectable marker gene (SMG) free transgenic plants. Replacement of selectable marker with screenable marker and some worldwide examples of SMG free crop plants produced by these strategies are also discussed. [ABSTRACT FROM AUTHOR]

Published
2024
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10. Diagnostic Assessments of Farmer-preferred Traits and Production Constraints of Cowpea in Zambia.

Author

Nkhoma, N., Shimelis, H., Laing, M., Mathew, I., and Shayanawako, A.

Subjects
*COWPEA, *INSECT diseases, *FARMERS, *INSECT pests, *VALUE chains, *CITIES & towns
Abstract

Background: Cowpea [Vigna unguiculata (L.) Walp.] in Zambia is a valuable source of cheap protein, complement to the food systems and value chains in rural and urban areas despite the low productivity. This study aimed to document the present level of cowpea production, identify constraints affecting cowpea production among smallholder farmers and prioritize trait preferences in a cowpea variety as a guide to pre-breeding programs in Zambia. Methods: Participatory rural appraisal (PRA) was used to collect data from cowpea production areas in Zambia's Eastern, Southern and Northern provinces. The PRA was conducted during the 2017/18 cropping season. Information was solicited from 187 farmers using interview questionnaires with a further focused group discussions with 7 groups. Result: Cowpea is perceived to be 'a woman's crop' in rural areas of Zambia but the present data showed that the frequency of female farmers who were directly involved in cowpea production in the study areas was relatively low at 44.00 per cent. About 93.60 per cent, the respondents were cultivating unimproved, local cowpea landraces, while the remainder (6.40 per cent) cultivated a few introduced varieties. The most important constraints of cowpea production in the study areas were identified by the respondents as poor varieties with low yield potential (45.10 per cent), pests and diseases (18.10 per cent) and the lack of modern production inputs (14.80 per cent). The farmers indicated that high yield potential, insect pest and disease resistance and good eating quality were the most important traits in a variety. [ABSTRACT FROM AUTHOR]

Published
2023
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16. Genetic diversity and population structure of groundnut (Arachis hypogaea L.) accessions using phenotypic traits and SSR markers: implications for rust resistance breeding

Author

Daudi, H., Shimelis, H., Mathew, I., Oteng‐Frimpong, R., Ojiewo, C., Varshney, R.K., Daudi, H., Shimelis, H., Mathew, I., Oteng‐Frimpong, R., Ojiewo, C., and Varshney, R.K.

Abstract

Groundnut (Arachis hypogaea L.) is a multi-purpose legume serving millions of farmers and their value chain actors globally. Use of old poor-performing cultivars contributes to low yields (< 1 t/ha) of groundnut in sub-Saharan Africa including Tanzania. The objectives of this study were to determine the extent of genetic variation among diverse groundnut collections using phenotypic traits and simple sequence repeat (SSR) markers to select distinct and complementary genotypes for breeding. One hundred and nineteen genotypes were evaluated under field conditions for agronomic traits and susceptibility to rust and leaf spot diseases. The study was conducted in two locations across two seasons. In addition, the 119 accessions were profiled with 13 selected SSR markers. Genotype and genotype by environment interaction effects were significant (p < 0.05) for days to flowering (DTF), late leaf spot score at 85 and 100 days after planting, pod yield (PDY), kernel yield (KY), hundred seed weight (HSW) and shelling percentage (SP). Principal components analysis revealed that plant stand, KY, SP, NPP (number of pods per plant), late leaf spot and rust disease scores accounted for the largest proportion of the total variation (71.9%) among the tested genotypes. Genotypes ICGV-SM 08587 and ICGV-SM 16579 had the most stable yields across the test environments. Moderate genetic variation was recorded with mean polymorphic information content of 0.34 and gene diversity of 0.63 using the SSR markers. The majority (74%) of genotypes showed high membership coefficients to their respective sub-populations, while 26% were admixtures after structure analysis. Much of the variation (69%) was found within populations due to genotypic differences. The present study identified genotypes ICGV-SM 06737, ICGV-SM 16575, ICG 12725 and ICGV-SM 16608 to be used for development of mapping population, which will be useful for groundnut improvement. This study provided a baseline information on chara

Published
2021

17. Racial and Ethnic Differences in Multigene Hereditary Cancer Panel Test Results for Women With Breast Cancer

Author

Yadav, S, LaDuca, H, Polley, EC, Hu, C, Niguidula, N, Shimelis, H, Lilyquist, J, Na, J, Lee, KY, Gutierrez, S, Yussuf, A, Hart, SN, Davis, BT, Chao, EC, Pesaran, T, Goldgar, DE, Dolinsky, JS, Couch, FJ, Yadav, S, LaDuca, H, Polley, EC, Hu, C, Niguidula, N, Shimelis, H, Lilyquist, J, Na, J, Lee, KY, Gutierrez, S, Yussuf, A, Hart, SN, Davis, BT, Chao, EC, Pesaran, T, Goldgar, DE, Dolinsky, JS, and Couch, FJ

Abstract

To evaluate the racial and ethnic differences in prevalence of germline pathogenic variants (PVs) and the effect of race and ethnicity on breast cancer (BC) risk among carriers, results of multigene testing of 77 900 women with BC (non-Hispanic White [NHW] = 57 003; Ashkenazi-Jewish = 4798; Black = 6722; Hispanic = 5194; and Asian = 4183) were analyzed, and the frequency of PVs in each gene were compared between BC patients (cases) and race- and ethnicity-matched gnomAD reference controls. Compared with NHWs, BRCA1 PVs were enriched in Ashkenazi-Jews and Hispanics, whereas CHEK2 PVs were statistically significantly lower in Blacks, Hispanics, and Asians (all 2-sided P < .05). In case-control studies, BARD1 PVs were associated with high risks (odds ratio > 4.00) of BC in Blacks, Hispanics, and Asians; ATM PVs were associated with increased risk of BC among all races and ethnicities except Asians, whereas CHEK2 and BRIP1 PVs were associated with increased risk of BC among NHWs and Hispanics only. These findings suggest a need for personalized management of BC risk in PV carriers based on race and ethnicity.

Published
2021

21. Can We Exploit Supernumerary Spikelet and Spike Branching Traits to Boots Bread Wheat (Triticum aestivum L.) Yield?

Author

Rizwan, M., Mahboob, W., Faheem, M., Shimelis, H., Hameed, A., Sial, M. A., Shokat, S., Rizwan, M., Mahboob, W., Faheem, M., Shimelis, H., Hameed, A., Sial, M. A., and Shokat, S.

Abstract

Maintaining population growth and competitiveness of arable lands is forcing plant scientist to develop novel ways to enhance grain yield per plant Several studies on wheat have demonstrated the manipulation of the number (supernumerary spikelet) and arrangement (spike branching) of spikelets. Several genes (FZP, ndsu, mrsl, qTS2A-1, bh, Ppd-1, bh(t), bh(m) sb 1, sb2, TFL) controlling supemumeraiy spikelet and spike branching trait have been reported. Different supemumeraiy spikelet and branched head wheat germplasm sources (Fen 33, SG203, R107, 166 Schakheli, AUS15910, Kalyan Sona, SWP-BSW1, BS-33, Yupi branching, WCB617 etc.) are also available in the world. However, little is known about the genetic underpinnings, mechanism, plant signaling and physiological aspects of these traits in wheat. Further, these traits are negatively correlated with grain weight and number of tillers per plant and are highly influenced by environmental factors, even tetraploid and hexaploid wheats with reported tendencies of ear branching show different expressions in different environments. In this review, which is a first review report to our knowledge, we have reported the possibilities to exploit these traits to double the number of grains per spike through the use of available supernumerary and branched head germplasm resources and how plant scientists can overcome the negative correlations to develop a sustainable phenotype.

Published
2020

22. Classification of variants of uncertain significance in BRCA1 and BRCA2 using personal and family history of cancer from individuals in a large hereditary cancer multigene panel testing cohort

Author

Li, H, LaDuca, H, Pesaran, T, Chao, EC, Dolinsky, JS, Parsons, M, Spurdle, AB, Polley, EC, Shimelis, H, Hart, SN, Hu, C, Couch, FJ, Goldgar, DE, Li, H, LaDuca, H, Pesaran, T, Chao, EC, Dolinsky, JS, Parsons, M, Spurdle, AB, Polley, EC, Shimelis, H, Hart, SN, Hu, C, Couch, FJ, and Goldgar, DE

Abstract

PURPOSE: Genetic testing of individuals often results in identification of genomic variants of unknown significance (VUS). Multiple lines of evidence are used to help determine the clinical significance of these variants. METHODS: We analyzed ~138,000 individuals tested by multigene panel testing (MGPT). We used logistic regression to predict carrier status based on personal and family history of cancer. This was applied to 4644 tested individuals carrying 2383 BRCA1/2 variants to calculate likelihood ratios informing pathogenicity for each. Heterogeneity tests were performed for specific classes of variants defined by in silico predictions. RESULTS: Twenty-two variants labeled as VUS had odds of >10:1 in favor of pathogenicity. The heterogeneity analysis found that among variants in functional domains that were predicted to be benign by in silico tools, a significantly higher proportion of variants were estimated to be pathogenic than previously indicated; that missense variants outside of functional domains should be considered benign; and that variants predicted to create de novo donor sites were also largely benign. CONCLUSION: The evidence presented here supports the use of personal and family history from MGPT in the classification of VUS and will be integrated into ongoing efforts to provide large-scale multifactorial classification.

Published
2020

23. The Contribution of Germline Predisposition Gene Mutations to Clinical Subtypes of Invasive Breast Cancer From a Clinical Genetic Testing Cohort

Author

Hu, C, Polley, EC, Yadav, S, Lilyquist, J, Shimelis, H, Na, J, Hart, SN, Goldgar, DE, Shah, S, Pesaran, T, Dolinsky, JS, LaDuca, H, Couch, FJ, Hu, C, Polley, EC, Yadav, S, Lilyquist, J, Shimelis, H, Na, J, Hart, SN, Goldgar, DE, Shah, S, Pesaran, T, Dolinsky, JS, LaDuca, H, and Couch, FJ

Abstract

BACKGROUND: The germline cancer predisposition genes associated with increased risk of each clinical subtype of breast cancer, defined by estrogen receptor (ER), progesterone receptor (PR), and HER2, are not well defined. METHODS: A total of 54 555 invasive breast cancer patients with 56 480 breast tumors were subjected to clinical hereditary cancer multigene panel testing. Heterogeneity for predisposition genes across clinical breast cancer subtypes was assessed by comparing mutation frequencies by gene among tumor subtypes and by association studies between each tumor subtype and reference controls. RESULTS: Mutations in 15 cancer predisposition genes were detected in 8.6% of patients with ER+/HER2-; 8.9% with ER+/HER2+; 7.7% with ER-/HER2+; and 14.4% of ER-/PR-/HER2- tumors. BRCA1, BRCA2, BARD1, and PALB2 mutations were enriched in ER- and HER2- tumors; RAD51C and RAD51D mutations were enriched in ER- tumors only; TP53 mutations were enriched in HER2+ tumors, and ATM and CHEK2 mutations were enriched in both ER+ and/or HER2+ tumors. All genes were associated with moderate (odds ratio > 2.00) or strong (odds ratio > 5.00) risks of at least one subtype of breast cancer in case-control analyses. Mutations in ATM, BARD1, BRCA1, BRCA2, CHEK2, PALB2, RAD51C, RAD51D, and TP53 had predicted lifetime absolute risks of at least 20.0% for breast cancer. CONCLUSIONS: Germline mutations in hereditary cancer panel genes confer subtype-specific risks of breast cancer. Combined tumor subtype, age at breast cancer diagnosis, and family history of breast and/or ovarian cancer information provides refined categorical estimates of mutation prevalence for women considering genetic testing.

Published
2020

24. Genome-wide association study of drought tolerance and biomass allocation in wheat

Author

Mathew, I., Shimelis, H., Shayanowako, A. I. T., Laing, M., and Chaplot, Vincent

Subjects
food and beverages
Abstract

Genome wide association studies (GWAS) are important in discerning the genetic architecture of complex traits such as biomass allocation for improving drought tolerance and carbon sequestration potential of wheat. The objectives of this study were to deduce the population structure and marker-trait association for biomass traits in wheat under droughtstressed and non-stressed conditions. A 100-wheat (Triticum aestivum L.) genotype panel was phenotyped for days to heading (DTH), days to maturity (DTM), shoot biomass (SB), root biomass (RB), root to shoot ratio (RS) and grain yield (GY). The panel was sequenced using 15,600 single nucleotide polymorphism (SNPs) markers and subjected to genetic analysis using the compressed mixed linear model (CMLM) at false discovery rate (FDR < 0.05). Population structure analysis revealed six sub-clusters with high membership ancestry coefficient of.0.65 to their assigned sub-clusters. A total of 75 significant marker-trait associations (MTAs) were identified with a linkage disequilibrium threshold of 0.38 at 5cM. Thirty-seven of the MTAs were detected under drought-stressed condition and 48% were on the B genome, where most quantitative trait loci (QTLs) for RB, SB and GY were previously identified. There were seven pleiotropic markers for RB and SB that may facilitate simultaneous selection. Thirty-seven putative candidate genes were mined by gene annotation on the IWGSC RefSeq 1.1. The significant MTAs observed in this study will be useful in devising strategies for marker-assisted breeding for simultaneous improvement of drought tolerance and to enhance C sequestration capacity of wheat.

Published
2019

28. Gene-panel testing of breast and ovarian cancer patients identifies a recurrent RAD51C duplication

Author

Pelttari, L. M., Shimelis, H., Toiminen, H., Kvist, A., Törngren, T., Borg, Å., Blomqvist, C., Bützow, R., Couch, F., Aittomäki, K., Nevanlinna, H., Department of Obstetrics and Gynecology, Clinicum, University of Helsinki, HUSLAB, Department of Oncology, Department of Pathology, Medicum, Kristiina Aittomäki / Principal Investigator, Department of Medical and Clinical Genetics, and HUS Comprehensive Cancer Center

Subjects
RISK, endocrine system diseases, RAD51C, 1184 Genetics, developmental biology, physiology, GERMLINE MUTATIONS, BRCA1, CHEK2-ASTERISK-1100DELC, FAMILIES, PARALOGS, breast cancer, ovarian cancer, 3123 Gynaecology and paediatrics, gene-panel, PATTERNS, CONFER SUSCEPTIBILITY, COMPLEXES, 3111 Biomedicine, skin and connective tissue diseases, POPULATION
Abstract

Gene-panel sequencing allows comprehensive analysis of multiple genes simultaneously and is now routinely used in clinical mutation testing of high-risk breast and ovarian cancer patients. However, only BRCA1 and BRCA2 are often analyzed also for large genomic changes. Here, we have analyzed 10 clinically relevant susceptibility genes in 95 breast or ovarian cancer patients with gene-panel sequencing including also copy number variants (CNV) analysis for genomic changes. We identified 12 different pathogenic BRCA1, BRCA2, TP53, PTEN, CHEK2, or RAD51C mutations in 18 of 95 patients (19%). BRCA1/2 mutations were observed in 8 patients (8.4%) and CHEK2 protein-truncating mutations in 7 patients (7.4%). In addition, we identified a novel duplication encompassing most of the RAD51C gene. We further genotyped the duplication in breast or ovarian cancer families (n=1149), in unselected breast (n=1729) and ovarian cancer cohorts (n=553), and in population controls (n=1273). Seven additional duplication carries were observed among cases but none among controls. The duplication associated with ovarian cancer risk (3/590 of all ovarian cancer patients, 0.5%, P=.032 compared with controls) and was found to represent a large fraction of all identified RAD51C mutations in the Finnish population. Our data emphasizes the importance of comprehensive mutation analysis including CNV detection in all the relevant genes.

Published
2018

29. Preliminary morphological characterization and evaluation of selected Bambara groundnut [Vigna subterranea (L.) Verdc.] genotypes for yield and yield related traits.

Author

Mohammed, M. S., Shimelis, H. A., and Laing, M. D.

Subjects
*BAMBARA groundnut, *BLACK gram, *PEANUTS, *PRINCIPAL components analysis, *GENOTYPES, *GERMPLASM conservation, *GERMPLASM
Abstract

Forty nine (49) Bambara groundnut genotypes derived from single plant selection of diverse origin were evaluated for yield and yield components using 26 yield and yield related traits. Highly significant (P<0.001) differences were detected among the genotypes for canopy spread, petiole length, weight of biomass, seed weight and seed height, while seedling emergence, pod weight, seed length and seed width were significantly different (P<0.05). Principal component analysis identified nine influential components whereby PC1 and PC2 highly contributed to the total variation at 19% and 14%, respectively. Leaf colour at emergence, petiole colour, leaf joint pigmentation and calyx colour were highly correlated with PC1, while seed length, seed width and seed height had strong association with PC2. Both the principal component and cluster analyses displayed common association among most of the genotypes for agronomic and seed yield traits. Genotypes that showed high seed yield performance and greater biomass production can be tested for large-scale production, breeding or germplasm conservation. [ABSTRACT FROM AUTHOR]

Published
2020
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32. Triple-Negative Breast Cancer Risk Genes Identified by Multigene Hereditary Cancer Panel Testing

Author

Shimelis, H, LaDuca, H, Hu, C, Hart, SN, Na, J, Thomas, A, Akinhanmi, M, Moore, RM, Brauch, H, Cox, A, Eccles, DM, Ewart-Toland, A, Fasching, PA, Fostira, F, Garber, J, Godwin, AK, Konstantopoulou, I, Nevanlinna, H, Sharma, P, Yannoukakos, D, Yao, S, Feng, B-J, Davis, BT, Lilyquist, J, Pesaran, T, Goldgar, DE, Polley, EC, Dolinsky, JS, Couch, FJ, Shimelis, H, LaDuca, H, Hu, C, Hart, SN, Na, J, Thomas, A, Akinhanmi, M, Moore, RM, Brauch, H, Cox, A, Eccles, DM, Ewart-Toland, A, Fasching, PA, Fostira, F, Garber, J, Godwin, AK, Konstantopoulou, I, Nevanlinna, H, Sharma, P, Yannoukakos, D, Yao, S, Feng, B-J, Davis, BT, Lilyquist, J, Pesaran, T, Goldgar, DE, Polley, EC, Dolinsky, JS, and Couch, FJ

Abstract

BACKGROUND: Germline genetic testing with hereditary cancer gene panels can identify women at increased risk of breast cancer. However, those at increased risk of triple-negative (estrogen receptor-negative, progesterone receptor-negative, human epidermal growth factor receptor-negative) breast cancer (TNBC) cannot be identified because predisposition genes for TNBC, other than BRCA1, have not been established. The aim of this study was to define the cancer panel genes associated with increased risk of TNBC. METHODS: Multigene panel testing for 21 genes in 8753 TNBC patients was performed by a clinical testing laboratory, and testing for 17 genes in 2148 patients was conducted by a Triple Negative Breast Cancer Consortium (TNBCC) of research studies. Associations between deleterious mutations in cancer predisposition genes and TNBC were evaluated using results from TNBC patients and reference controls. RESULTS: Germline pathogenic variants in BARD1, BRCA1, BRCA2, PALB2, and RAD51D were associated with high risk (odds ratio > 5.0) of TNBC and greater than 20% lifetime risk for overall breast cancer among Caucasians. Pathogenic variants in BRIP1, RAD51C, and TP53 were associated with moderate risk (odds ratio > 2) of TNBC. Similar trends were observed for the African American population. Pathogenic variants in these TNBC genes were detected in 12.0% (3.7% non-BRCA1/2) of all participants. CONCLUSIONS: Multigene hereditary cancer panel testing can identify women with elevated risk of TNBC due to mutations in BARD1, BRCA1, BRCA2, PALB2, and RAD51D. These women can potentially benefit from improved screening, risk management, and cancer prevention strategies. Patients with mutations may also benefit from specific targeted therapeutic strategies.

Published
2018

33. Multigene Hereditary Cancer Panels Reveal High-Risk Pancreatic Cancer Susceptibility Genes

Author

Hu, C, LaDuca, H, Shimelis, H, Polley, EC, Lilyquist, J, Hart, SN, Na, J, Thomas, A, Lee, KY, Davis, BT, Black, MH, Pesaran, T, Goldgar, DE, Dolinsky, JS, Couch, FJ, Hu, C, LaDuca, H, Shimelis, H, Polley, EC, Lilyquist, J, Hart, SN, Na, J, Thomas, A, Lee, KY, Davis, BT, Black, MH, Pesaran, T, Goldgar, DE, Dolinsky, JS, and Couch, FJ

Abstract

PURPOSE: The relevance of inherited pathogenic mutations in cancer predisposition genes in pancreatic cancer is not well understood. We aimed to assess the characteristics of patients with pancreatic cancer referred for hereditary cancer genetic testing and to estimate the risk of pancreatic cancer associated with mutations in panel-based cancer predisposition genes in this high-risk population. METHODS: Patients with pancreatic cancer (N = 1,652) were identified from a 140,000-patient cohort undergoing multigene panel testing of predisposition genes between March 2012 and June 2016. Gene-level mutation frequencies relative to Exome Aggregation Consortium and Genome Aggregation Database reference controls were assessed. RESULTS: The frequency of germline cancer predisposition gene mutations among patients with pancreatic cancer was 20.73%. Mutations in ATM, BRCA2, CDKN2A, MSH2, MSH6, PALB2, and TP53 were associated with high pancreatic cancer risk (odds ratio, > 5), and mutations in BRCA1 were associated with moderate risk (odds ratio, > 2). In a logistic regression model adjusted for age at diagnosis and family history of cancer, ATM and BRCA2 mutations were associated with personal history of breast or pancreatic cancer, whereas PALB2 mutations were associated with family history of breast or pancreatic cancer. CONCLUSION: These findings provide insight into the spectrum of mutations expected in patients with pancreatic cancer referred for cancer predisposition testing. Mutations in eight genes confer high or moderate risk of pancreatic cancer and may prove useful for risk assessment for pancreatic and other cancers. Family and personal histories of breast cancer are strong predictors of germline mutations.

Published
2018

37. Comparison between random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers with high resolution melt analyses in genetic variation analysis among selected sorghum genotypes

Author

Mofokeng, MA, Watson, G, Shimelis, H, and Tongoona, P

Subjects
Genetic diversity, high resolution melt analysis, RAPD, simple sequence repeat, sorghum
Abstract

Understanding the genetic diversity of germplasm is essential in plant breeding programmes and germplasm management. Molecular markers are efficient and effective tools widely used for assessing genetic diversity among crop genotypes. Recently, high resolution melt analysis (HRM) has been reported for detecting genetic variability. However, there is limited information on the use of HRM in conjunction with other molecular marker techniques for assessing genetic variation in sorghum [Sorghum bicolor (L.) Moench]. This study was conducted to compare random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers with HRM analyses to determine genetic variation among selected sorghum genotypes. Eight diverse sorghum accessions obtained from the plant genetic resources, Department of Agriculture, Forestry and Fisheries/South Africa were subjected to both analyses. DNA was extracted from fresh leaves of the eight accessions and amplified using three RAPD and three SSR primers. The HRM analysis was performed and temperature normalised melting curves and difference plots were created and results compared. Both the molecular markers and HRM revealed variations among the accessions. The HRM melting profiles fairly well correlated with results from the RAPD and SSR analysis. The clustering of sorghum accessions using SSR marker highly corresponded with the HRM analysis. Therefore, the HRM can be a useful tool in genetic diversity and classification of sorghum genotypes without post-PCR analysis or processing.Key words: Genetic diversity, high resolution melt analysis, RAPD, simple sequence repeat, sorghum.

Published
2016

38. BRCA2 polymorphic stop codon K3326X and the risk of breast, prostate, and ovarian cancers

Author

Meeks, H.D., Song, H.L., Michailidou, K., Bolla, M.K., Dennis, J., Wang, Q., Barrowdale, D., Frost, D., McGuffog, L., Ellis, S., Feng, B.J., Buys, S.S., Hopper, J.L., Southey, M.C., Tesoriero, A., James, P.A., Bruinsma, F., Campbell, I.G., Broeks, A., Schmidt, M.K., Hogervorst, F.B.L., Beckman, M.W., Fasching, P.A., Fletcher, O., Johnson, N., Sawyer, E.J., Riboli, E., Banerjee, S., Menon, U., Tomlinson, I., Burwinkel, B., Hamann, U., Marme, F., Rudolph, A., Janavicius, R., Tihomirova, L., Tung, N., Garber, J., Cramer, D., Terry, K.L., Poole, E.M., Tworoger, S.S., Dorfling, C.M., Rensburg, E.J. van, Godwin, A.K., Guenel, P., Truong, T., Stoppa-Lyonnet, D., Damiola, F., Mazoyer, S., Sinilnikova, O.M., Isaacs, C., Maugard, C., Bojesen, S.E., Flyger, H., Gerdes, A.M., Hansen, T.V.O., Jensen, A., Kjaer, S.K., Hogdall, C., Hogdall, E., Pedersen, I.S., Thomassen, M., Benitez, J., Gonzalez-Neira, A., Osorio, A., Hoya, M. de la, Segura, P.P., Diez, O., Lazaro, C., Brunet, J., Anton-Culver, H., Eunjung, L., John, E.M., Neuhausen, S.L., Ding, Y.C., Castillo, D., Weitzel, J.N., Ganz, P.A., Nussbaum, R.L., Chan, S.B., Karlan, B.Y., Lester, J., Wu, A., Gayther, S., Ramus, S.J., Sieh, W., Whittermore, A.S., Monteiro, A.N.A., Phelan, C.M., Terry, M.B., Piedmonte, M., Offit, K., Robson, M., Levine, D., Moysich, K.B., Cannioto, R., Olson, S.H., Daly, M.B., Nathanson, K.L., Domchek, S.M., Lu, K.H., Liang, D., Hildebrant, M.A.T., Ness, R., Modugno, F., Pearce, L., Goodman, M.T., Thompson, P.J., Brenner, H., Butterbach, K., Meindl, A., Hahnen, E., Wappenschmidt, B., Brauch, H., Bruning, T., Blomqvist, C., Khan, S., Nevanlinna, H., Pelttari, L.M., Aittomaki, K., Butzow, R., Bogdanova, N.V., Dork, T., Lindblom, A., Margolin, S., Rantala, J., Kosma, V.M., Mannermaa, A., Lambrechts, D., Neven, P., Claes, K.B.M., Maerken, T. van, Chang-Claude, J., Flesch-Janys, D., Heitz, F., Varon-Mateeva, R., Peterlongo, P., Radice, P., Viel, A., Barile, M., Peissel, B., Manoukian, S., Montagna, M., Oliani, C., Peixoto, A., Teixeira, M.R., Collavoli, A., Hallberg, E., Olson, J.E., Goode, E.L., Hart, S.N., Shimelis, H., Cunningham, J.M., Giles, G.G., Milne, R.L., Healey, S., Tucker, K., Haiman, C.A., Henderson, B.E., Goldberg, M.S., Tischkowitz, M., Simard, J., Soucy, P., Eccles, D.M., N. le, Borresen-Dale, A.L., Kristensen, V., Salvesen, H.B., Bjorge, L., Bandera, E.V., Risch, H., Zheng, W., Beeghly-Fadiel, A., Cai, H., Pylkas, K., Tollenaar, R.A.E.M., Ouweland, A.M.W. van der, Andrulis, I.L., Knight, J.A., Narod, S., Devilee, P., Winqvist, R., Figueroa, J., Greene, M.H., Mai, P.L., Loud, J.T., Garcia-Closas, M., Schoemaker, M.J., Czene, K., Darabi, H., McNeish, I., Siddiquil, N., Glasspool, R., Kwong, A., Park, S.K., Teo, S.H., Yoon, S.Y., Matsuo, K., Hosono, S., Woo, Y.L., Gao, Y.T., Foretova, L., Singer, C.F., Rappaport-Feurhauser, C., Friedman, E., Laitman, Y., Rennert, G., Imyanitov, E.N., Hulick, P.J., Olopade, O.I., Senter, L., Olah, E., Doherty, J.A., Schildkraut, J., 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Greece [ 232 ] Duke Univ, Med Ctr, Dept Obstet & Gynecol, Durham, NC 27710 USA

Subjects
0301 basic medicine, Oncology, Male, Cancer Research, endocrine system diseases, LOCI, Estrogen receptor, FAMILY-HISTORY, Prostate cancer, 0302 clinical medicine, Ovarian Neoplasms/pathology, Prostate, Risk Factors, Brjóstakrabbamein, Odds Ratio, skin and connective tissue diseases, Ovarian Neoplasms, Women's cancers Radboud Institute for Molecular Life Sciences [Radboudumc 17], Prostatic Neoplasms/genetics, Research Support, Non-U.S. Gov't, SINGLE-NUCLEOTIDE POLYMORPHISMS, Middle Aged, BRCA2 Protein/genetics, PANCREATIC-CANCER, 3. Good health, SUSCEPTIBILITY GENE, medicine.anatomical_structure, Urological cancers Radboud Institute for Health Sciences [Radboudumc 15], 030220 oncology & carcinogenesis, Codon, Terminator, Female, Risk Factors Substances, Adult, medicine.medical_specialty, Heterozygote, Breast Neoplasms, Blöðruhálskirtilskrabbamein, Breast Neoplasms/genetics, Biology, Polymorphism, Single Nucleotide, Risk Assessment, Article, Ovarian Neoplasms/genetics, 03 medical and health sciences, Breast cancer, SDG 3 - Good Health and Well-being, Research Support, N.I.H., Extramural, Internal medicine, Pancreatic cancer, Krabbameinsrannsóknir, medicine, Journal Article, Humans, Genetic Predisposition to Disease, Neoplasm Invasiveness, Lysine/genetics, Krabbamein, Aged, Gynecology, BRCA2 Protein, Proportional hazards model, Lysine, DNA RECOMBINATION, CONSORTIUM, GERM-LINE MUTATION, Prostatic Neoplasms, Odds ratio, Arfgengi, medicine.disease, ESTROGEN-RECEPTOR, 030104 developmental biology, Logistic Models, PTT12, Eggjastokkar, FANCONI-ANEMIA, Ovarian cancer
Abstract

Contains fulltext : 172007.pdf (Publisher’s version ) (Closed access) BACKGROUND: The K3326X variant in BRCA2 (BRCA2*c.9976A>T; p.Lys3326*; rs11571833) has been found to be associated with small increased risks of breast cancer. However, it is not clear to what extent linkage disequilibrium with fully pathogenic mutations might account for this association. There is scant information about the effect of K3326X in other hormone-related cancers. METHODS: Using weighted logistic regression, we analyzed data from the large iCOGS study including 76 637 cancer case patients and 83 796 control patients to estimate odds ratios (ORw) and 95% confidence intervals (CIs) for K3326X variant carriers in relation to breast, ovarian, and prostate cancer risks, with weights defined as probability of not having a pathogenic BRCA2 variant. Using Cox proportional hazards modeling, we also examined the associations of K3326X with breast and ovarian cancer risks among 7183 BRCA1 variant carriers. All statistical tests were two-sided. RESULTS: The K3326X variant was associated with breast (ORw = 1.28, 95% CI = 1.17 to 1.40, P = 5.9x10(-) (6)) and invasive ovarian cancer (ORw = 1.26, 95% CI = 1.10 to 1.43, P = 3.8x10(-3)). These associations were stronger for serous ovarian cancer and for estrogen receptor-negative breast cancer (ORw = 1.46, 95% CI = 1.2 to 1.70, P = 3.4x10(-5) and ORw = 1.50, 95% CI = 1.28 to 1.76, P = 4.1x10(-5), respectively). For BRCA1 mutation carriers, there was a statistically significant inverse association of the K3326X variant with risk of ovarian cancer (HR = 0.43, 95% CI = 0.22 to 0.84, P = .013) but no association with breast cancer. No association with prostate cancer was observed. CONCLUSIONS: Our study provides evidence that the K3326X variant is associated with risk of developing breast and ovarian cancers independent of other pathogenic variants in BRCA2. Further studies are needed to determine the biological mechanism of action responsible for these associations.

Published
2016
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39. GENE FLOW FROM MAJOR GENETICALLY MODIFIED CROPS AND STRATEGIES FOR CONTAINMENT AND MITIGATION OF TRANSGENE ESCAPE: A REVIEW.

Author

RIZWAN, M., HUSSAIN, M., SHIMELIS, H., HAMEED, M. U., ATIF, R. M., AZHAR, M. T., QAMAR, Z., and ASIF, M.

Subjects
GENE flow, TRANSGENIC plants, ECOLOGICAL zones, TRANSGENE expression, ORGANIC farming, ESCAPES, FLOW meters
Abstract

Recent advancements in biotechnology resulted in rapid adoption of genetically modified (GM) crops in the agriculture systems. At the same time, transgene escape has also been reported and examples reveal global dimension of the problem. Pollen mediated gene flow (PMGF) is the major pathway for transgene escape. Almost all transgenes have been escaped into their Non-GM counterpart and wild relatives. Although gene flow varies between species, crops, and ecological zones/environments but intraspecific gene flow (> 10%) is not uncommon in adjacent populations. Whereas in outcrossing species, 1% gene flow at thousand meters’ isolation is not unusual, and magnitude is even higher than the mutation rate. It is well documented that transgene flow is deteriorating different production systems in agriculture and famers choice to cultivate GM, conventional and organic crops. If comprehensive policy is not implemented, then in future it will be difficult to detect and remove transgenes from the environment; if unexpected problems arise. [ABSTRACT FROM AUTHOR]

Published
2019
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40. Male breast cancer in a multi-gene panel testing cohort: insights and unexpected results

Author

Pritzlaff, M, Summerour, P, McFarland, R, Li, S, Reineke, P, Dolinsky, JS, Goldgar, DE, Shimelis, H, Couch, FJ, Chao, EC, LaDuca, H, Pritzlaff, M, Summerour, P, McFarland, R, Li, S, Reineke, P, Dolinsky, JS, Goldgar, DE, Shimelis, H, Couch, FJ, Chao, EC, and LaDuca, H

Abstract

PURPOSE: Genetic predisposition to male breast cancer (MBC) is not well understood. The aim of this study was to better define the predisposition genes contributing to MBC and the utility of germline multi-gene panel testing (MGPT) for explaining the etiology of MBCs. METHODS: Clinical histories and molecular results were retrospectively reviewed for 715 MBC patients who underwent MGPT from March 2012 to June 2016. RESULTS: The detection rate of MGPT was 18.1% for patients tested for variants in 16 breast cancer susceptibility genes and with no prior BRCA1/2 testing. BRCA2 and CHEK2 were the most frequently mutated genes (11.0 and 4.1% of patients with no prior BRCA1/2 testing, respectively). Pathogenic variants in BRCA2 [odds ratio (OR) = 13.9; p = 1.92 × 10-16], CHEK2 (OR = 3.7; p = 6.24 × 10-24), and PALB2 (OR = 6.6, p = 0.01) were associated with significantly increased risks of MBC. The average age at diagnosis of MBC was similar for patients with (64 years) and without (62 years) pathogenic variants. CHEK2 1100delC carriers had a significantly lower average age of diagnosis (n = 7; 54 years) than all others with pathogenic variants (p = 0.03). No significant differences were observed between history of additional primary cancers (non-breast) and family history of male breast cancer for patients with and without pathogenic variants. However, patients with pathogenic variants in BRCA2 were more likely to have a history of multiple primary breast cancers. CONCLUSION: These data suggest that all MBC patients regardless of age of diagnosis, history of multiple primary cancers, or family history of MBC should be offered MGPT.

Published
2017

41. Production hygiene and training influences on rural small-scale organic farmer practices: South Africa

Author

Mdluli, F, Thamaga-Chitja, J, Schmidt, S, and Shimelis, H

Abstract

In view of frequently reported foodborne disease outbreaks caused by contaminated fresh produce, consumers have a preference for foods meeting requisite hygiene standards. Production of good quality fresh produce is thus critical for market access and food security, especially for rural, small-scale farmers. Microbiological product quality in this South African sector is crucial, given the policy drive to develop small-scale farming to reinforce household food security and poverty reduction. Farming practices and methods, throughout the fresh produce value chain impact final product quality, determining its market success. The aim of the study was therefore to determine the extent to which training in organic farming methods, including modules such as the Importance of Production Hygiene’ influenced the hygienic farming practices of small-scale, organic farmers in eTholeni, uMbumbulu, KwaZulu-Natal, South Africa. Questionnaires were administered to 73 uncertified, organic farmers; analysis showed that only 33 farmers were trained and supplied the local Agri-Hub, whereas 40 had not received training. The questionnaire probed respondent hygiene practices. Data analysis included descriptive statistics, such as the Chi-square test and a logistic regression model. Descriptive analysis indicated that most farmers (60%) were female, most of whom (73%) were over 40 years old. The logistic regression indicated that factors such as farmer training and prior experience in the farming sector had a significant influence on hygiene practices, both at 5% significance levels. These results emphasize the importance of training, education and farming experience in implementing good hygiene practices in small-scale farming. It is recommended therefore, that South African Agricultural Extension policies should advocate for small-scale farmer training. This training should include market-focused farmer training to supply produce markets with high quality fresh produce; and subsistence focused training for household food security.

Published
2014

43. Abstract S2-01: Breast cancer risks associated with mutations in cancer predisposition genes identified by clinical genetic testing of 60,000 breast cancer patients

Author

Couch, FJ, primary, Hu, C, additional, Lilyquist, J, additional, Shimelis, H, additional, Akinhanmi, M, additional, Na, J, additional, Polley, EC, additional, Hart, SN, additional, McFarland, R, additional, LaDuca, H, additional, Huether, R, additional, Goldgar, DE, additional, and Dolinsky, JS, additional

Published
2017
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45. BRCA2 Polymorphic Stop Codon K3326X and the Risk of Breast, Prostate, and Ovarian Cancers

Author

Meeks, H.D. (Huong D.), Song, H. (Honglin), Michailidou, K. (Kyriaki), Bolla, M.K. (Manjeet), Dennis, J. (Joe), Wang, Q. (Qing), Barrowdale, D. (Daniel), Frost, D. (Debra), McGuffog, L. (Lesley), Ellis, S.D. (Steve), Feng, B. (Bingjian), Buys, S.S. (Saundra), Hopper, J.L. (John), Southey, M.C. (Melissa), Tesoriero, A. (Andrea), James, M. (Margaret), Bruinsma, F. (Fiona), Campbell, I. (Ian), Broeks, A. (Annegien), Schmidt, M.K. (Marjanka), Hogervorst, F.B.L. (Frans), Beckmann, M.W. (Matthias), Fasching, P.A. (Peter), Fletcher, O. (Olivia), Johnson, N. (Nichola), Sawyer, E.J. (Elinor), Riboli, E. (Elio), Banerjee, S. (Susana), Menon, U. (Usha), Tomlinson, I. (Ian), Burwinkel, B. (Barbara), Hamann, U. (Ute), Marme, F. (Federick), Rudolph, A. (Anja), Janavicius, R. (Ramunas), Tihomirova, L. (Laima), Tung, N. (Nadine), Garber, J. (Judy), Cramer, D. (Daniel), Terry, K.L. (Kathryn), Poole, E.M. (Elizabeth), Tworoger, S. (Shelley), Dorfling, C.M. (Cecilia), Rensburg, E.J. (Elizabeth) van, Godwin, A.K. (Andrew K.), Guénel, P. (Pascal), Truong, T. (Thérèse), Stoppa-Lyonnet, D. (Dominique), Damiola, F. (Francesca), Mazoyer, S. (Sylvie), Sinilnikova, O. (Olga), Isaacs, C. (Claudine), Maugard, C., Bojesen, S.E. (Stig), Flyger, H. (Henrik), Gerdes, A-M. (Anne-Marie), Hansen, T.V.O. (Thomas), Jensen, A. (Allen), Kjaer, M. (Michael), Høgdall, C.K. (Claus), Høgdall, E. (Estrid), Pedersen, I.S. (Inge Sokilde), Thomassen, M. (Mads), Benítez, J. (Javier), González-Neira, A. (Anna), Osorio, A. (Ana), Hoya, M.D.L. (Miguel De La), Segura, P.P. (Pedro Perez), Díez, O. (Orland), Lázaro, C. (Conxi), Brunet, J. (Joan), Anton-Culver, H. (Hoda), Eunjung, L. (Lee), John, E.M. (Esther), Neuhausen, S.L. (Susan), Ding, Y.C. (Yuan), Castillo, D. (Danielle), Weitzel, J.N. (Jeffrey), Ganz, P.A. (Patricia A.), Nussbaum, R. (Robert), Chan, S. (Salina), Karlan, B.Y. (Beth Y.), Lester, K.J. (Kathryn), Wu, A. (Anna), Gayther, S.A. (Simon), Ramus, S.J. (Susan), Sieh, W. (Weiva), Whittermore, A.S. (Alice S.), Monteiro, A.N.A. (Alvaro N.A.), Phelan, C. (Catherine), Terry, M.B. (Mary Beth), Piedmonte, M. (Marion), Offit, K. (Kenneth), Robson, M. (Mark), Levine, D.A. (Douglas), Moysich, K.B. (Kirsten B.), Cannioto, R. (Rikki), Olson, S.H. (Sara), Daly, M.B. (Mary B.), Nathanson, K.L. (Katherine), Domchek, S.M. (Susan), Lu, K.H. (Karen), Liang, D. (Dong), Hildebrant, M.A.T. (Michelle A.T.), Ness, R.B. (Roberta), Modugno, F. (Francesmary), Pearce, L. (Leigh), Goodman, M.T. (Marc T.), Thompson, P.J. (Pamela J.), Brenner, H. (Hermann), Butterbach, K. (Katja), Meindl, A. (Alfons), Hahnen, E. (Eric), Wapenschmidt, B. (Barbara), Brauch, H. (Hiltrud), Brüning, T. (Thomas), Blomqvist, C. (Carl), Khan, S. (Sofia), Nevanlinna, H. (Heli), Pelttari, L.M. (Liisa), Aittomäki, K. (Kristiina), Butzow, R. (Ralf), Bogdanova, N.V. (Natalia), Dörk, T. (Thilo), Lindblom, A. (Annika), Margolin, S. (Sara), Rantala, J. (Johanna), Kosma, V-M. (Veli-Matti), Mannermaa, A. (Arto), Lambrechts, D. (Diether), Neven, P. (Patrick), Claes, K.B.M. (Kathleen B.M.), Van Maerken, T. (Tom), Chang-Claude, J. (Jenny), Flesch-Janys, D. (Dieter), Heitz, P.U., Varon-Mateeva, R. (Raymonda), Peterlongo, P. (Paolo), Radice, P. (Paolo), Viel, A. (Alessandra), Barile, M. (Monica), Peissel, B. (Bernard), Manoukian, S. (Siranoush), Montagna, M. (Marco), Oliani, C. (Cristina), Peixoto, A. (Ana), Teixeira, P.J., Collavoli, A. (Anita), Hallberg, B. (Boubou), Olson, J.E. (Janet), Goode, E.L. (Ellen L.), Hart, S.N. (Steven N.), Shimelis, H. (Hermela), Cunningham, J.M. (Julie), Giles, G.G. (Graham), Milne, R.L. (Roger), Healey, S. (Sue), Tucker, K. (Kathy), Haiman, C.A. (Christopher A.), Henderson, B.E. (Brian), Goldberg, M.S. (Mark), Tischkowitz, M. (Marc), Simard, J. (Jacques), Soucy, P. (Penny), Eccles, D. (Diana), Le, N. (Nhu), Borresen-Dale, A.-L. (Anne-Lise), Kristensen, V. (Vessela), Salvesen, H.B. (Helga), Bjorge, L. (Line), Bandera, E.V. (Elisa), Risch, H. (Harvey), Zheng, W. (Wei), Beeghly-Fadiel, A. (Alicia), Cai, H. (Hui), Pykäs, K. (Katri), Tollenaar, R.A.E.M. (Rob), Ouweland, A.M.W. (Ans) van den, Andrulis, I.L. (Irene), Knight, J.A. (Julia A.), Narod, S. (Steven), Devilee, P. (Peter), Winqvist, R. (Robert), Figueroa, J.D. (Jonine), Greene, M.H. (Mark H.), Mai, P.L. (Phuong), Loud, J.T. (Jennifer), García-Closas, M. (Montserrat), Schoemaker, M. (Minouk), Czene, K. (Kamila), Darabi, H. (Hatef), McNeish, I. (Iain), Siddiquil, N. (Nadeem), Glasspool, R. (Rosalind), Kwong, A. (Ava), Park, S.K. (Sue K.), Teo, S.-H. (Soo-Hwang), Yoon, S.-Y. (Sook-Yee), Matsuo, K. (Keitaro), Hosono, N. (Naoya), Woo, Y.L. (Yin Ling), Gao, Y. (Ying), Foretova, L. (Lenka), Singer, C.F. (Christian), Rappaport-Feurhauser, C. (Christine), Friedman, E. (Eitan), Laitman, Y. (Yael), Rennert, G. (Gad), Imyanitov, E.N. (Evgeny), Hulick, P.J. (Peter), Olopade, O.I. (Olufunmilayo I.), Senter, L. (Leigha), Olah, E. (Edith), Doherty, J.A. (Jennifer A.), Schildkraut, J.M. (Joellen), Koppert, L.B. (Linetta), Kiemeney, L.A.L.M. (Bart), Massuger, L.F. (Leon), Cook, L.S. (Linda S.), Pejovic, T. (Tanja), Li, J. (Jingmei), Borg, Å. (Åke), Öfverholm, A. (Anna), Rossing, M.A. (Mary Anne), Wentzensen, N. (N.), Henriksson, K. (Karin), Cox, A. (Angela), Cross, S.S. (Simon), Pasini, B. (Barbara), Shah, M. (Mitul), Kabisch, M. (Maria), Torres, D. (Diana), Jakubowska, A. (Anna), Lubinski, J. (Jan), Gronwald, J. (Jacek), Agnarsson, B.A. (Bjarni), Kupryjanczyk, J. (Jolanta), Moes-Sosnowska, J. (Joanna), Fostira, F. (Florentia), Konstantopoulou, I. (I.), Slager, S. (Susan), Jones, M. (Michael), Antoniou, A.C. (Antonis), Berchuck, A. (Andrew), Swerdlow, A.J. (Anthony ), Chenevix-Trench, G. (Georgia), Dunning, A.M. (Alison), Pharoah, P.D.P. (Paul), Hall, P. (Per), Easton, D.F. (Douglas F.), Couch, F.J. (Fergus), Spurdle, A.B. (Amanda), Goldgar, D. (David), Meeks, H.D. (Huong D.), Song, H. (Honglin), Michailidou, K. (Kyriaki), Bolla, M.K. (Manjeet), Dennis, J. (Joe), Wang, Q. (Qing), Barrowdale, D. (Daniel), Frost, D. (Debra), McGuffog, L. (Lesley), Ellis, S.D. (Steve), Feng, B. (Bingjian), Buys, S.S. (Saundra), Hopper, J.L. (John), Southey, M.C. (Melissa), Tesoriero, A. (Andrea), James, M. (Margaret), Bruinsma, F. (Fiona), Campbell, I. (Ian), Broeks, A. (Annegien), Schmidt, M.K. (Marjanka), Hogervorst, F.B.L. (Frans), Beckmann, M.W. (Matthias), Fasching, P.A. (Peter), Fletcher, O. (Olivia), Johnson, N. (Nichola), Sawyer, E.J. (Elinor), Riboli, E. (Elio), Banerjee, S. (Susana), Menon, U. (Usha), Tomlinson, I. (Ian), Burwinkel, B. (Barbara), Hamann, U. (Ute), Marme, F. (Federick), Rudolph, A. (Anja), Janavicius, R. (Ramunas), Tihomirova, L. (Laima), Tung, N. (Nadine), Garber, J. (Judy), Cramer, D. (Daniel), Terry, K.L. (Kathryn), Poole, E.M. (Elizabeth), Tworoger, S. (Shelley), Dorfling, C.M. (Cecilia), Rensburg, E.J. (Elizabeth) van, Godwin, A.K. (Andrew K.), Guénel, P. (Pascal), Truong, T. (Thérèse), Stoppa-Lyonnet, D. (Dominique), Damiola, F. (Francesca), Mazoyer, S. (Sylvie), Sinilnikova, O. (Olga), Isaacs, C. (Claudine), Maugard, C., Bojesen, S.E. (Stig), Flyger, H. (Henrik), Gerdes, A-M. (Anne-Marie), Hansen, T.V.O. (Thomas), Jensen, A. (Allen), Kjaer, M. (Michael), Høgdall, C.K. (Claus), Høgdall, E. (Estrid), Pedersen, I.S. (Inge Sokilde), Thomassen, M. (Mads), Benítez, J. (Javier), González-Neira, A. (Anna), Osorio, A. (Ana), Hoya, M.D.L. (Miguel De La), Segura, P.P. (Pedro Perez), Díez, O. (Orland), Lázaro, C. (Conxi), Brunet, J. (Joan), Anton-Culver, H. (Hoda), Eunjung, L. (Lee), John, E.M. (Esther), Neuhausen, S.L. (Susan), Ding, Y.C. (Yuan), Castillo, D. (Danielle), Weitzel, J.N. (Jeffrey), Ganz, P.A. (Patricia A.), Nussbaum, R. (Robert), Chan, S. (Salina), Karlan, B.Y. (Beth Y.), Lester, K.J. (Kathryn), Wu, A. (Anna), Gayther, S.A. (Simon), Ramus, S.J. (Susan), Sieh, W. (Weiva), Whittermore, A.S. (Alice S.), Monteiro, A.N.A. (Alvaro N.A.), Phelan, C. (Catherine), Terry, M.B. (Mary Beth), Piedmonte, M. (Marion), Offit, K. (Kenneth), Robson, M. (Mark), Levine, D.A. (Douglas), Moysich, K.B. (Kirsten B.), Cannioto, R. (Rikki), Olson, S.H. (Sara), Daly, M.B. (Mary B.), Nathanson, K.L. (Katherine), Domchek, S.M. (Susan), Lu, K.H. (Karen), Liang, D. (Dong), Hildebrant, M.A.T. (Michelle A.T.), Ness, R.B. (Roberta), Modugno, F. (Francesmary), Pearce, L. (Leigh), Goodman, M.T. (Marc T.), Thompson, P.J. (Pamela J.), Brenner, H. (Hermann), Butterbach, K. (Katja), Meindl, A. (Alfons), Hahnen, E. (Eric), Wapenschmidt, B. (Barbara), Brauch, H. (Hiltrud), Brüning, T. (Thomas), Blomqvist, C. (Carl), Khan, S. (Sofia), Nevanlinna, H. (Heli), Pelttari, L.M. (Liisa), Aittomäki, K. (Kristiina), Butzow, R. (Ralf), Bogdanova, N.V. (Natalia), Dörk, T. (Thilo), Lindblom, A. (Annika), Margolin, S. (Sara), Rantala, J. (Johanna), Kosma, V-M. (Veli-Matti), Mannermaa, A. (Arto), Lambrechts, D. (Diether), Neven, P. (Patrick), Claes, K.B.M. (Kathleen B.M.), Van Maerken, T. (Tom), Chang-Claude, J. (Jenny), Flesch-Janys, D. (Dieter), Heitz, P.U., Varon-Mateeva, R. (Raymonda), Peterlongo, P. (Paolo), Radice, P. (Paolo), Viel, A. (Alessandra), Barile, M. (Monica), Peissel, B. (Bernard), Manoukian, S. (Siranoush), Montagna, M. (Marco), Oliani, C. (Cristina), Peixoto, A. (Ana), Teixeira, P.J., Collavoli, A. (Anita), Hallberg, B. (Boubou), Olson, J.E. (Janet), Goode, E.L. (Ellen L.), Hart, S.N. (Steven N.), Shimelis, H. (Hermela), Cunningham, J.M. (Julie), Giles, G.G. (Graham), Milne, R.L. (Roger), Healey, S. (Sue), Tucker, K. (Kathy), Haiman, C.A. (Christopher A.), Henderson, B.E. (Brian), Goldberg, M.S. (Mark), Tischkowitz, M. (Marc), Simard, J. (Jacques), Soucy, P. (Penny), Eccles, D. (Diana), Le, N. (Nhu), Borresen-Dale, A.-L. (Anne-Lise), Kristensen, V. (Vessela), Salvesen, H.B. (Helga), Bjorge, L. (Line), Bandera, E.V. (Elisa), Risch, H. (Harvey), Zheng, W. (Wei), Beeghly-Fadiel, A. (Alicia), Cai, H. (Hui), Pykäs, K. (Katri), Tollenaar, R.A.E.M. (Rob), Ouweland, A.M.W. (Ans) van den, Andrulis, I.L. (Irene), Knight, J.A. (Julia A.), Narod, S. (Steven), Devilee, P. (Peter), Winqvist, R. (Robert), Figueroa, J.D. (Jonine), Greene, M.H. (Mark H.), Mai, P.L. (Phuong), Loud, J.T. (Jennifer), García-Closas, M. (Montserrat), Schoemaker, M. (Minouk), Czene, K. (Kamila), Darabi, H. (Hatef), McNeish, I. (Iain), Siddiquil, N. (Nadeem), Glasspool, R. (Rosalind), Kwong, A. (Ava), Park, S.K. (Sue K.), Teo, S.-H. (Soo-Hwang), Yoon, S.-Y. (Sook-Yee), Matsuo, K. (Keitaro), Hosono, N. (Naoya), Woo, Y.L. (Yin Ling), Gao, Y. (Ying), Foretova, L. (Lenka), Singer, C.F. (Christian), Rappaport-Feurhauser, C. (Christine), Friedman, E. (Eitan), Laitman, Y. (Yael), Rennert, G. (Gad), Imyanitov, E.N. (Evgeny), Hulick, P.J. (Peter), Olopade, O.I. (Olufunmilayo I.), Senter, L. (Leigha), Olah, E. (Edith), Doherty, J.A. (Jennifer A.), Schildkraut, J.M. (Joellen), Koppert, L.B. (Linetta), Kiemeney, L.A.L.M. (Bart), Massuger, L.F. (Leon), Cook, L.S. (Linda S.), Pejovic, T. (Tanja), Li, J. (Jingmei), Borg, Å. (Åke), Öfverholm, A. (Anna), Rossing, M.A. (Mary Anne), Wentzensen, N. (N.), Henriksson, K. (Karin), Cox, A. (Angela), Cross, S.S. (Simon), Pasini, B. (Barbara), Shah, M. (Mitul), Kabisch, M. (Maria), Torres, D. (Diana), Jakubowska, A. (Anna), Lubinski, J. (Jan), Gronwald, J. (Jacek), Agnarsson, B.A. (Bjarni), Kupryjanczyk, J. (Jolanta), Moes-Sosnowska, J. (Joanna), Fostira, F. (Florentia), Konstantopoulou, I. (I.), Slager, S. (Susan), Jones, M. (Michael), Antoniou, A.C. (Antonis), Berchuck, A. (Andrew), Swerdlow, A.J. (Anthony ), Chenevix-Trench, G. (Georgia), Dunning, A.M. (Alison), Pharoah, P.D.P. (Paul), Hall, P. (Per), Easton, D.F. (Douglas F.), Couch, F.J. (Fergus), Spurdle, A.B. (Amanda), and Goldgar, D. (David)

Abstract

Background: The K3326X variant in BRCA2 (BRCA2∗c.9976A>T p.Lys3326∗rs11571833) has been found to be associated with small increased risks of breast cancer. However, it is not clear to what extent linkage disequilibrium with fully pathogenic mutations might account for this association. There is scant information about the effect of K3326X in other hormonerelated cancers. Methods: Using weighted logistic regression, we analyzed data from the large iCOGS study including 76637 cancer case patients and 83796 control patients to estimate odds ratios (ORw) and 95% confidence intervals (CIs) for K3326X variant carriers in relation to breast, ovarian, and prostate cancer risks, with weights defined as probability of not having a pathogenic BRCA2 variant. Using Cox proportional hazards modeling, we also examined the associations of K3326X with breast and ovarian cancer risks among 7183 BRCA1 variant carriers. All statistical tests were two-sided. Results: The K3326X variant was associated with breast (ORw = 1.28, 95% CI = 1.17 to 1.40, P = 5.9×10-6) and invasive ovarian cancer (ORw = 1.26, 95% CI = 1.10 to 1.43, P = 3.8×10-3). These associations were stronger for serous ovarian cancer and for estrogen receptor-negative breast cancer (ORw = 1.46, 95% CI = 1.2 to 1.70, P = 3.4×10-5 and ORw = 1.50, 95% CI = 1.28 to

Published
2016
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46. APPRAISAL OF MAJOR DETERMINANTS OF RICE PRODUCTION AND FARMERS' CHOICE OF RICE IDEOTYPES IN SOUTH SUDAN: IMPLICATIONS FOR BREEDING AND POLICY INTERVENTIONS.

Author

MOGGA, M., SIBIYA, J., SHIMELIS, H., LAMO, J., and OCHANDA, N.

Abstract

SUMMARY: Rice (Oryza sativa L.) is an important staple crop in South Sudan. Current rice consumption in the country is approximately 23,000 mg year−1 of which more than 75% is imported. We investigated farmers' perceived rice production and productivity constraints and choice of rice ideotypes across rainfed and irrigated rice agro-ecologies in South Sudan to guide breeding and policy interventions. Data were gathered through participatory rural approaches and a formal structured survey involving 136 rice farmers from major rice growing areas of South Sudan. Farmers generally cultivated old rice varieties with low yields varying from 0.4 to 1.6 mg ha−1. Pair-wise ranking based on respondents score indicated yield, early maturity, cooking and eating quality, nutritional importance and drought tolerance as the most desirable traits of rice ideotypes. Further, imported rice varieties were best ranked for their sweet and appealing taste, rich aroma, grain shape and size, swelling capacity and non-stickiness during cooking. Major perceived constraints to rice production were unreliable rainfall, poor access to credit facilities, poor soil and water management practices, poor rice storage facilities, inadequate and poor processing machines as well as limited technical skills in rice production. The results show a need for integration of farmers' and stakeholders' preferences in variety development process and the desirability of releasing site-specific rice cultivars given the differences in bio-physical, socio-cultural and farmers preferences across major rice growing areas of South Sudan. [ABSTRACT FROM AUTHOR]

Published
2019
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47. Aneuploids of wheat and chromosomal localization of genes

Author

Shimelis, H and Spies, JJ

Subjects
Aneuploids, Chinese spring, chromosome, cytogenetics, Langdon durum, monosomics, substitution lines
Abstract

Identification of useful major or minor genes is an important step in crop improvement programs. The chromosome location of such genes is critical for effective utilization and subsequent manipulation. Further, chromosomal localization will lead to the identification of genomic regions responsible for the expression of the trait of interest. DNA markers linked to these traits could be identified and used for marker-assisted breeding. Various cytogenetic stocks and techniques have been previously reported useful in localizing genes on wheat chromosomes. The objective of this paper is to assemble the most commonly used cytogenetic methods for the chromosomal localization of major genes in wheat including Chinese spring (CS) monosomics (Triticum aestivum, 2n=6x-1=41) and Langdon durum Dgenome disomic substitution lines (Triticum turgidum, 2n=4x-2+2=28). The paper reviewed and outlined the use and development of monomosic and substitution lines in a suitable genetic background for genetic analysis in wheat. The information may assist wheat researchers to locate and utilize newly identified genes in breeding programs.Key words: Aneuploids, Chinese spring, chromosome, cytogenetics, Langdon durum, monosomics, substitution lines.

Published
2013

50. Genetic Diversity of Maize Genotypes with Variable Resistance to Striga asiaticaBased on SSR Markers

Author

Shayanowako, A. I. T., Shimelis, H., Laing, M. D., and Mwadzingeni, L.

Abstract

Genetic diversity among breeding populations is key in plant breeding programs. This study aimed to determine the extent of genetic diversity among 37 diverse maize genotypes using simple sequence repeat (SSR) markers. The maize genotypes were selected based on their variable resistance to Striga asiatica. Maize genotypes were fingerprinted using 18 polymorphic SSR markers. Marker and population diversity parameters were computed. A total of 191 alleles were detected and the number of effective alleles varied from 2 to 21 per locus with a mean of 11. The polymorphic information content (PIC) of the SSR markers varied from 0.59 to 0.96, with a mean of 0.80. Significant differences were observed among populations, individuals and within individuals. Within and among individual variances accounted for 85% and 13% of the total gene diversity. The genotypes were grouped into three main genetic clusters, which were not influenced by genotype origin. Mean genetic distance (0.43) and low geneflow (0.18) were observed among the populations. High mean genetic identity (0.65) was recorded, indicating potential genetic ‘bottleneck’ among the selected germplasm. The following open pollinated varieties; Border King, Colorado, CIMMYT’s ZM OPVs, Mac Pearl, Shesha, Nel Choice, Natal 8Lines, Nel Choice QPM, Hickory King, Kep Select, Obatanpa and the Strigaresistant synthetic variety DSTRYSYN15 were selected from different clusters for breeding.

Published
2018
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